X chromosome variant genotypes from vcf files

Question

[SGMS]

Hi everyone,

My question is pretty simple but I'm struggling to find a recent effective answer. I want to count the heterozygous and homozygous genotypes on X chromosome from a standard vcf file. The only answer I can find is posted here: Genotype representation for male chromosome X and Y

They should normally be haploid instead of diploid. Has anyone come across this problem recently? If so, how did you solve this?

Any help would be greatly appreciated.

Thank you in advance.

Answer 1

[Pierre Lindenbaum]

they should normally be haploid instead of diploid. Has anyone come across this problem recently?

call has haploid in the non-PAR regions for men on X and Y